mnase  (New England Biolabs)


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  • 99
    Name:
    ShortCut RNase III
    Description:
    ShortCut RNase III 1 000 units
    Catalog Number:
    M0245L
    Price:
    494
    Size:
    1 000 units
    Category:
    Ribonucleases RNase
    Score:
    85
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    Structured Review

    New England Biolabs mnase
    ShortCut RNase III
    ShortCut RNase III 1 000 units
    https://www.bioz.com/result/mnase/product/New England Biolabs
    Average 99 stars, based on 49 article reviews
    Price from $9.99 to $1999.99
    mnase - by Bioz Stars, 2019-11
    99/100 stars

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    Related Articles

    Centrifugation:

    Article Title: Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum
    Article Snippet: Parasites were lysed with 200 strokes in a prechilled Dounce homogenizer and nuclei collected by centrifugation, cleaned through a 0.34 M sucrose cushion, and resuspended in 1 ml of prechilled buffer A supplemented with 2 mM CaCl2 plus protease inhibitors. .. Mononucleosomes were prepared from freshly isolated nuclei by digestion with 4 U MNase (NEB) for different amounts of time at 33°C; digestion was stopped by adding 10 mM EGTA pH 8.0.

    Article Title: HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
    Article Snippet: For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract. .. For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract.

    Article Title: Formation of Mobile Chromatin-Associated Nuclear Foci Containing HIV-1 Vpr and VPRBP Is Critical for the Induction of G2 Cell Cycle Arrest
    Article Snippet: Insoluble cell debris, including chromatin, was pelleted by centrifugation (2500g for 10 minutes). .. Pellets were washed once with nuclease buffer (50 mM Tris pH 8.0, 5 mM CaCl2 , and 100 µg/ml BSA), split in two, and resuspended in nuclease buffer alone or nuclease buffer containing 200 U/ml microccocal nuclease (New England Biolabs, Ipswich, MA, USA).

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: Chromatin from 5×106 cells per antibody that had been cross-linked with 0.5% formaldehyde for 10 min was isolated by sonication with a Branson sonifier (10 pulses of 10″ at setting 4) in Lysis buffer (50 mM Hepes-KOH, pH 7.5, 1% TritonX-100, 0.1% SDS) and centrifugation for 10′ at 21,000×g . .. To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA.

    Article Title: cGAS surveillance of micronuclei links genome instability to innate immunity
    Article Snippet: Nuclei were resuspended at 20 A260 in buffer NBR2 and digested with MNase (400 units.ml-1 nuclei; NEB) for 10 min at room temperature. .. The reaction was stopped by adding EDTA to 10 mM, nuclei were re-suspend in 500 µl of TEP20N (10 mM Tris, pH8; 1 mM EDTA; 20 mM NaCl, 0.5 µM PMSF, 0.05% NP40) and incubated at 4°C overnight.

    Article Title: USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization
    Article Snippet: The lysate was cleared with centrifugation at 2000 × g for 5 min at 4 °C, and then collected and washed with lysis buffer twice. .. The nuclear pellet was suspended with 50 μl glycerol buffer (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 5 mM MgAc2 and 25% (vol/vol) glycerol), mixed with equal volume of 2 × MNase buffer (50 mM KCl, 8 mM MgCl2 , 2 mM CaCl2 , and 100 mM Tris-HCl, pH 7.5) and incubated at 37 °C for 5 min with 40 gel Unit of MNase (NEB) per 100 μl of total reaction volume.

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C. .. The samples were diluted by half with 2 × ChIP dilution buffer (2% Triton X-100, 280 mM NaCl, 80 mM Tris-HCl [pH8.0] in ChIP buffer from the Active Motif kit) and further sonicated for two pulses of 25 s each.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: After disruption with a dounce homogenizer, nuclei were collected by centrifugation. .. Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C.

    Amplification:

    Article Title: Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning
    Article Snippet: Briefly, cells were fixed for 10 min with 1% formaldehyde, crosslinking was quenched with 125 mM glycine for 5 min and incubated in permeabilization buffer (150 mM sucrose, 80 mM KCl, 35 mM HEPES [pH 7.4], 5 mM K2 HPO4 , 5 mM MgCl2 and 0.5 mM CaCl2 , 0.05% L-α-lysophosphatidylcholine) for 1 min. Chromatin was digested with 50 units/ml MNase (New England Biolabs) in 150 mM sucrose, 50 mM NaCl, 50 mM Tris–HCl [pH 7.4] and 2 mM CaCl2 for 20 min at room temperature. .. Briefly, cells were fixed for 10 min with 1% formaldehyde, crosslinking was quenched with 125 mM glycine for 5 min and incubated in permeabilization buffer (150 mM sucrose, 80 mM KCl, 35 mM HEPES [pH 7.4], 5 mM K2 HPO4 , 5 mM MgCl2 and 0.5 mM CaCl2 , 0.05% L-α-lysophosphatidylcholine) for 1 min. Chromatin was digested with 50 units/ml MNase (New England Biolabs) in 150 mM sucrose, 50 mM NaCl, 50 mM Tris–HCl [pH 7.4] and 2 mM CaCl2 for 20 min at room temperature.

    Electrophoresis:

    Article Title: An Improved Strategy to Recover Large Fragments of Functional Human Neutrophil Extracellular Traps
    Article Snippet: In a first set of experiments, 4 μg of purified λDNA (Invitrogen) was treated with 4 U/mL DNase I (Sigma Aldrich), 4 U/mL MNase (New England BioLabs, France), or 4 U/mL Alu I (New England BioLabs) for 20 min at 37°C. .. In a first set of experiments, 4 μg of purified λDNA (Invitrogen) was treated with 4 U/mL DNase I (Sigma Aldrich), 4 U/mL MNase (New England BioLabs, France), or 4 U/mL Alu I (New England BioLabs) for 20 min at 37°C.

    Article Title: USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization
    Article Snippet: The nuclear pellet was suspended with 50 μl glycerol buffer (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 5 mM MgAc2 and 25% (vol/vol) glycerol), mixed with equal volume of 2 × MNase buffer (50 mM KCl, 8 mM MgCl2 , 2 mM CaCl2 , and 100 mM Tris-HCl, pH 7.5) and incubated at 37 °C for 5 min with 40 gel Unit of MNase (NEB) per 100 μl of total reaction volume. .. The reaction was stopped by adding EDTA to a final concentration of 10 mM.

    Incubation:

    Article Title: Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum
    Article Snippet: Briefly, schizont‐stage parasites of WT or WT + PfH3p‐HA were isolated from infected erythrocytes by saponin lysis, resuspended in 1 ml of buffer A (10 mM HEPES, pH 7.9, 10 mM KCl, 1.5 mM MgCl2 ) supplemented with protease inhibitors (Complete, Roche), and incubated for 30 min at 4°C. .. Mononucleosomes were prepared from freshly isolated nuclei by digestion with 4 U MNase (NEB) for different amounts of time at 33°C; digestion was stopped by adding 10 mM EGTA pH 8.0.

    Article Title: HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
    Article Snippet: Next, CaCl2 was added to 5 mM with 30 U of RQ1 DNase (Promega) and incubated for 15 min at 25°C. .. For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract.

    Article Title: Formation of Mobile Chromatin-Associated Nuclear Foci Containing HIV-1 Vpr and VPRBP Is Critical for the Induction of G2 Cell Cycle Arrest
    Article Snippet: Pellets were washed once with nuclease buffer (50 mM Tris pH 8.0, 5 mM CaCl2 , and 100 µg/ml BSA), split in two, and resuspended in nuclease buffer alone or nuclease buffer containing 200 U/ml microccocal nuclease (New England Biolabs, Ipswich, MA, USA). .. Pellets were washed once with nuclease buffer (50 mM Tris pH 8.0, 5 mM CaCl2 , and 100 µg/ml BSA), split in two, and resuspended in nuclease buffer alone or nuclease buffer containing 200 U/ml microccocal nuclease (New England Biolabs, Ipswich, MA, USA).

    Article Title: CAL1 is the Drosophila CENP-A assembly factor
    Article Snippet: To assemble CENP-A nucleosomes, Drosophila CENP-A101–225 –H4–Cal11–160 (3.8 µM), Alexa Fluor 488–labeled H2A–H2B (2.5 µM), and 147-bp Widom 601 DNA (0.72 µM) were mixed and incubated for 1 h under low salt buffer conditions. .. MNase digestion of nucleosomes was conducted by incubating nucleosomes (∼60 nM) with 2,000 U/ml MNase (New England Biolabs, Inc.) for 30–120 s. After the reactions were stopped by addition of 20 mM EDTA, the samples were treated with 2% SDS and 0.4 mg/ml proteinase K for 30 min at 55°C.

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA. .. Digested chromatin was diluted 3-fold with High Salt ChIP buffer (10 mM Tris-HCl, pH 8, 400 mM NaCl, 1% TritonX-100, 2 mM EDTA, Complete protease inhibitors w/o EDTA (Roche)) to yield 600 μl total volume and incubated overnight at 4°C with either 5 μl of anti-H3 (39163, Active Motif, concentration is not known), 4 μg of anti-H2A.Z (ab4174; Abcam), 1 μg of anti-H3K4me1 (ab8895; Abcam), 1 μg of anti-H3K4me3 (ab8580; Abcam) or 1 μg of H3K27ac (ab4729; Abcam).

    Article Title: Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder
    Article Snippet: The digestion was carried out with MNase (New England BioLabs) at 4 U MNase per 200 μl of reaction buffer at 25°C for the indicated period of time. .. The digestion was carried out with MNase (New England BioLabs) at 4 U MNase per 200 μl of reaction buffer at 25°C for the indicated period of time.

    Article Title: USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization
    Article Snippet: The lysate was cleared with centrifugation at 2000 × g for 5 min at 4 °C, and then collected and washed with lysis buffer twice. .. The nuclear pellet was suspended with 50 μl glycerol buffer (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 5 mM MgAc2 and 25% (vol/vol) glycerol), mixed with equal volume of 2 × MNase buffer (50 mM KCl, 8 mM MgCl2 , 2 mM CaCl2 , and 100 mM Tris-HCl, pH 7.5) and incubated at 37 °C for 5 min with 40 gel Unit of MNase (NEB) per 100 μl of total reaction volume. .. The reaction was stopped by adding EDTA to a final concentration of 10 mM.

    Article Title: Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning
    Article Snippet: Positions of rDNA promoter-bound nucleosomes were analyzed by LM-PCR as described ( ). .. Briefly, cells were fixed for 10 min with 1% formaldehyde, crosslinking was quenched with 125 mM glycine for 5 min and incubated in permeabilization buffer (150 mM sucrose, 80 mM KCl, 35 mM HEPES [pH 7.4], 5 mM K2 HPO4 , 5 mM MgCl2 and 0.5 mM CaCl2 , 0.05% L-α-lysophosphatidylcholine) for 1 min. Chromatin was digested with 50 units/ml MNase (New England Biolabs) in 150 mM sucrose, 50 mM NaCl, 50 mM Tris–HCl [pH 7.4] and 2 mM CaCl2 for 20 min at room temperature. .. After incubation for 6 h at 65°C, DNA was purified and mononucleosome-sized fragments were recovered from 2% agarose gels with QIAquick Gel Extraction Kit (QIAGEN).

    Article Title: The Initial Response of a Eukaryotic Replisome to DNA Damage
    Article Snippet: After chromatin assembly CaCl2 was added to 5 mM. .. 20 μL was collected and 1 μL 20-fold diluted MNase (100 U) (New England Biolabs M0247, diluted in 1X MNase buffer, New England Biolabs B0247) added and the mixture incubated at 37°C for 5 min. .. The reaction was stopped with 20 mM EGTA.

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: Sonication was carried out using a Misonix 2000 Sonicator (Misonix) at power 7. .. After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C. .. The reaction was stopped by adding 20 mM EGTA.

    Modification:

    Article Title: cGAS surveillance of micronuclei links genome instability to innate immunity
    Article Snippet: Soluble chromatin was prepared from NIH3T3 cells as previously described , but an increased concentration of NP40 detergent (0.2%) was used in buffer NBB and buffer NBR was replaced by buffer NBR2 (buffer NBR modified to contain 1 mM MgCl2 and 1 mM CaCl2). .. Nuclei were resuspended at 20 A260 in buffer NBR2 and digested with MNase (400 units.ml-1 nuclei; NEB) for 10 min at room temperature.

    Transfection:

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
    Article Snippet: To quantify RBPJ binding to nucleosomes, Flag-RBPJ was transfected into 293 cells. .. Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    Concentration Assay:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: To quench the reactions 12 μl of 10 % solution of phenol in ethanol and EGTA to final concentration 25 mM were added on ice to each aliquot. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C.

    Article Title: cGAS surveillance of micronuclei links genome instability to innate immunity
    Article Snippet: Soluble chromatin was prepared from NIH3T3 cells as previously described , but an increased concentration of NP40 detergent (0.2%) was used in buffer NBB and buffer NBR was replaced by buffer NBR2 (buffer NBR modified to contain 1 mM MgCl2 and 1 mM CaCl2). .. Nuclei were resuspended at 20 A260 in buffer NBR2 and digested with MNase (400 units.ml-1 nuclei; NEB) for 10 min at room temperature.

    Protease Inhibitor:

    Article Title: HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
    Article Snippet: The composition of the SDS lysis buffer was 0.5% SDS, 50mM Tris pH 6.8, 1mM EDTA, 0.125 mg/ml Heparin, 1mM DTT, 1mM PMSF and 1X protease inhibitor (Calbiochem), while RIPA correction buffer was 1.25% NP40, 0.625% sodium deoxycholate, 62.5 mM Tris pH 8.0, 2.25 mM EDTA, 187.5 mM NaCl, 0.125 mg/ml Heparin, 1mM DTT, 1mM PMSF, with 1X protease inhibitors. .. For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract.

    Article Title: m6A-dependent regulation of messenger RNA stability
    Article Snippet: 1 mL lysis buffer (10 mM Tris, pH 7.4, 150 mM KCl, 5 mM MgCl2 , 100 µg/mL CHX, 0.5% Triton-X-100, freshly add 1:100 protease inhibitor, 40 U/mL SUPERasin) was added to suspend the cells and then kept on ice for 15 min with occasional pipetting and rotating. .. 40 µL MNase buffer and 3 µL MNase (6000 gel units, NEB) was added to Portion II .

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: Pooled cortices from 10 males and 10 females (total 20 mice) were cross-linked with 1% formaldehyde in PBS for 15 min at room temperature and ChIP was performed using the ChIP-IT High Sensitivity kit (Active Motif) per the manufacturer's instructions, with some modifications: after homogenization using a Dounce homogenizer, nuclei were washed in LB0 buffer (20 mM Tris-HCl [pH7.5], 10 mM NaCl, 1 mM EDTA, 0.2% NP-40, 1 mM PMSF) and resuspended in MNase buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 2.5 mM MgCl2 , 0.1% NP-40, 1 mM DTT, 1 mM PMSF), provided with cOmplete™ EDTA-free protease inhibitor cocktail (Roche Diagnostics). .. After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    Footprinting:

    Article Title: Histone H3 phosphorylation near the nucleosome dyad alters chromatin structure
    Article Snippet: Paragraph title: MNase footprinting ... Reactions were carried out in an initial volume of 10 μl with 10 nM nucleosomes and 0–40 U/ml of MNase (New England Biolabs) in 20 mM Tris, pH 8.0, 0.5 mM CaCl2 at 37°C to prevent H3(T118ph) nucleosome disassembly.

    Infection:

    Article Title: Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum
    Article Snippet: Briefly, schizont‐stage parasites of WT or WT + PfH3p‐HA were isolated from infected erythrocytes by saponin lysis, resuspended in 1 ml of buffer A (10 mM HEPES, pH 7.9, 10 mM KCl, 1.5 mM MgCl2 ) supplemented with protease inhibitors (Complete, Roche), and incubated for 30 min at 4°C. .. Mononucleosomes were prepared from freshly isolated nuclei by digestion with 4 U MNase (NEB) for different amounts of time at 33°C; digestion was stopped by adding 10 mM EGTA pH 8.0.

    Generated:

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C. .. After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    Imaging:

    Article Title: CAL1 is the Drosophila CENP-A assembly factor
    Article Snippet: The nucleosomes were analyzed by 6% native PAGE and stained by SYBR gold; the incorporation of H2A–H2B was confirmed by fluorescence imaging of the gel for Alexa Fluor 488. .. MNase digestion of nucleosomes was conducted by incubating nucleosomes (∼60 nM) with 2,000 U/ml MNase (New England Biolabs, Inc.) for 30–120 s. After the reactions were stopped by addition of 20 mM EDTA, the samples were treated with 2% SDS and 0.4 mg/ml proteinase K for 30 min at 55°C.

    Polymerase Chain Reaction:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C.

    Article Title: Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning
    Article Snippet: Briefly, cells were fixed for 10 min with 1% formaldehyde, crosslinking was quenched with 125 mM glycine for 5 min and incubated in permeabilization buffer (150 mM sucrose, 80 mM KCl, 35 mM HEPES [pH 7.4], 5 mM K2 HPO4 , 5 mM MgCl2 and 0.5 mM CaCl2 , 0.05% L-α-lysophosphatidylcholine) for 1 min. Chromatin was digested with 50 units/ml MNase (New England Biolabs) in 150 mM sucrose, 50 mM NaCl, 50 mM Tris–HCl [pH 7.4] and 2 mM CaCl2 for 20 min at room temperature. .. Briefly, cells were fixed for 10 min with 1% formaldehyde, crosslinking was quenched with 125 mM glycine for 5 min and incubated in permeabilization buffer (150 mM sucrose, 80 mM KCl, 35 mM HEPES [pH 7.4], 5 mM K2 HPO4 , 5 mM MgCl2 and 0.5 mM CaCl2 , 0.05% L-α-lysophosphatidylcholine) for 1 min. Chromatin was digested with 50 units/ml MNase (New England Biolabs) in 150 mM sucrose, 50 mM NaCl, 50 mM Tris–HCl [pH 7.4] and 2 mM CaCl2 for 20 min at room temperature.

    Article Title: The Initial Response of a Eukaryotic Replisome to DNA Damage
    Article Snippet: 20 μL was collected and 1 μL 20-fold diluted MNase (100 U) (New England Biolabs M0247, diluted in 1X MNase buffer, New England Biolabs B0247) added and the mixture incubated at 37°C for 5 min. .. 20 μL was collected and 1 μL 20-fold diluted MNase (100 U) (New England Biolabs M0247, diluted in 1X MNase buffer, New England Biolabs B0247) added and the mixture incubated at 37°C for 5 min.

    Sonication:

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
    Article Snippet: For ChIP-PCR and for RNA Pol II and H3K9ac ChIP-seq, the MNAse digestion step was replaced with a sonication step in 0.12% SDS followed by 5× dilution with concentrated ChIP buffer. .. Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: Chromatin from 5×106 cells per antibody that had been cross-linked with 0.5% formaldehyde for 10 min was isolated by sonication with a Branson sonifier (10 pulses of 10″ at setting 4) in Lysis buffer (50 mM Hepes-KOH, pH 7.5, 1% TritonX-100, 0.1% SDS) and centrifugation for 10′ at 21,000×g . .. To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA.

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: Sonication was carried out using a Misonix 2000 Sonicator (Misonix) at power 7. .. After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    Affinity Purification:

    Article Title: HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
    Article Snippet: For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract. .. After clarification of the lysate by three successive centrifugation steps at 21K x g for 10 min, the lysate was pre-cleared and the ORF57-RNA complexes were immunoprecipitated with protein A Dynabeads (Invitrogen).

    Binding Assay:

    Article Title: Formation of Mobile Chromatin-Associated Nuclear Foci Containing HIV-1 Vpr and VPRBP Is Critical for the Induction of G2 Cell Cycle Arrest
    Article Snippet: Paragraph title: Chromatin binding assays ... Pellets were washed once with nuclease buffer (50 mM Tris pH 8.0, 5 mM CaCl2 , and 100 µg/ml BSA), split in two, and resuspended in nuclease buffer alone or nuclease buffer containing 200 U/ml microccocal nuclease (New England Biolabs, Ipswich, MA, USA).

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
    Article Snippet: To quantify RBPJ binding to nucleosomes, Flag-RBPJ was transfected into 293 cells. .. Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: Chromatin from 5×106 cells per antibody that had been cross-linked with 0.5% formaldehyde for 10 min was isolated by sonication with a Branson sonifier (10 pulses of 10″ at setting 4) in Lysis buffer (50 mM Hepes-KOH, pH 7.5, 1% TritonX-100, 0.1% SDS) and centrifugation for 10′ at 21,000×g . .. To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA. .. Digested chromatin was diluted 3-fold with High Salt ChIP buffer (10 mM Tris-HCl, pH 8, 400 mM NaCl, 1% TritonX-100, 2 mM EDTA, Complete protease inhibitors w/o EDTA (Roche)) to yield 600 μl total volume and incubated overnight at 4°C with either 5 μl of anti-H3 (39163, Active Motif, concentration is not known), 4 μg of anti-H2A.Z (ab4174; Abcam), 1 μg of anti-H3K4me1 (ab8895; Abcam), 1 μg of anti-H3K4me3 (ab8580; Abcam) or 1 μg of H3K27ac (ab4729; Abcam).

    ChIP-sequencing:

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
    Article Snippet: Paragraph title: ChIP-seq and ChIP-PCR ... Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    DNA Sequencing:

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C. .. After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA).

    In Vivo:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: Paragraph title: In vivo MNase digestion ... The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C.

    Fluorescence:

    Article Title: CAL1 is the Drosophila CENP-A assembly factor
    Article Snippet: The nucleosomes were analyzed by 6% native PAGE and stained by SYBR gold; the incorporation of H2A–H2B was confirmed by fluorescence imaging of the gel for Alexa Fluor 488. .. MNase digestion of nucleosomes was conducted by incubating nucleosomes (∼60 nM) with 2,000 U/ml MNase (New England Biolabs, Inc.) for 30–120 s. After the reactions were stopped by addition of 20 mM EDTA, the samples were treated with 2% SDS and 0.4 mg/ml proteinase K for 30 min at 55°C.

    Magnetic Beads:

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA. .. For all other ChIP experiments isolated chromatin was directly diluted with High Salt ChIP buffer and incubated with either 1 μg of anti-PolI antibody (sc-56767), 6 μg anti-TBP (sc-204), 4 μg anti-PU.1 (sc-352), 4 μg anti-C/EBPβ (sc-150), 6 μg anti-NFκB (sc-372), 5 μg anti-c-Jun (sc-45), 6 μg anti-p300 (sc-585) or 10 μg anti-IRF3 (sc-9082) all from Santa Cruz Biotechnologies.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C. .. MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM.

    Isolation:

    Article Title: Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum
    Article Snippet: Parasites were lysed with 200 strokes in a prechilled Dounce homogenizer and nuclei collected by centrifugation, cleaned through a 0.34 M sucrose cushion, and resuspended in 1 ml of prechilled buffer A supplemented with 2 mM CaCl2 plus protease inhibitors. .. Mononucleosomes were prepared from freshly isolated nuclei by digestion with 4 U MNase (NEB) for different amounts of time at 33°C; digestion was stopped by adding 10 mM EGTA pH 8.0. .. After spinning out debris at 18,800 g for 15 min at 4°C, the supernatant was analyzed for the presence of mononucleosomes by extracting DNA and resolving it on a 2% agarose gel stained with ethidium bromide.

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: Chromatin from 5×106 cells per antibody that had been cross-linked with 0.5% formaldehyde for 10 min was isolated by sonication with a Branson sonifier (10 pulses of 10″ at setting 4) in Lysis buffer (50 mM Hepes-KOH, pH 7.5, 1% TritonX-100, 0.1% SDS) and centrifugation for 10′ at 21,000×g . .. To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA. .. Digested chromatin was diluted 3-fold with High Salt ChIP buffer (10 mM Tris-HCl, pH 8, 400 mM NaCl, 1% TritonX-100, 2 mM EDTA, Complete protease inhibitors w/o EDTA (Roche)) to yield 600 μl total volume and incubated overnight at 4°C with either 5 μl of anti-H3 (39163, Active Motif, concentration is not known), 4 μg of anti-H2A.Z (ab4174; Abcam), 1 μg of anti-H3K4me1 (ab8895; Abcam), 1 μg of anti-H3K4me3 (ab8580; Abcam) or 1 μg of H3K27ac (ab4729; Abcam).

    Article Title: Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder
    Article Snippet: In brief, cell nuclei were isolated using hypotonic buffer (10 mM HEPES, pH 7.9, 10 mM KCl, 1.5 mM MgCl2 , 0.34 M sucrose, 10% glycerol, and 1 mM dithiothreitol (DTT)) and 0.1% Triton X-100. .. The digestion was carried out with MNase (New England BioLabs) at 4 U MNase per 200 μl of reaction buffer at 25°C for the indicated period of time.

    Article Title: ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites
    Article Snippet: Paragraph title: Isolation of nucleosomal DNA by micrococcal nuclease (MNase) digestion ... Digestion of chromatin from untreated, siCTRL- or siAGO2-treated HeLa S3 cells (2 × 106 ) was performed with 50 U of MNase (New England Biolabs) in 300 μl of permeabilization buffer (15 mM Tris–HCl pH 7.4, 300 mM sucrose, 60 mM KCl, 15 mM NaCl, 4 mM CaCl2 , 0.5 mM EGTA, 0.2% NP-40, 0.5 mM β-mercaptoethanol) for 20 min at 37°C.

    Clarification Assay:

    Article Title: HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
    Article Snippet: For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract. .. For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract.

    Purification:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: As control in sequence analysis, we used DNA fragments obtained from in vitro MNase digestion of purified wild type genomic DNA. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C. .. The aliquots were taken out and reaction was stopped at different time points by adding EDTA and incubating with proteinase K for 1 hour at 65 °C.

    Article Title: An Improved Strategy to Recover Large Fragments of Functional Human Neutrophil Extracellular Traps
    Article Snippet: All images were acquired with a Plan-Apochromat 63X/1.4 NO oil immersion objective, using two light-emitting diodes (365 and 470 nm) for excitation and two bandpass filters (445/450 and 530/550 nm) to collect blue and green fluorescence, respectively. .. In a first set of experiments, 4 μg of purified λDNA (Invitrogen) was treated with 4 U/mL DNase I (Sigma Aldrich), 4 U/mL MNase (New England BioLabs, France), or 4 U/mL Alu I (New England BioLabs) for 20 min at 37°C. .. The samples were then loaded on 0.8% agarose gels (w/v) prepared in Tris-acetate-EDTA buffer containing 0.5 μg/mL ethidium bromide (Invitrogen).

    Article Title: cGAS surveillance of micronuclei links genome instability to innate immunity
    Article Snippet: Paragraph title: Chromatin synthesis and purification ... Nuclei were resuspended at 20 A260 in buffer NBR2 and digested with MNase (400 units.ml-1 nuclei; NEB) for 10 min at room temperature.

    Article Title: Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder
    Article Snippet: The digestion was carried out with MNase (New England BioLabs) at 4 U MNase per 200 μl of reaction buffer at 25°C for the indicated period of time. .. The digestion was carried out with MNase (New England BioLabs) at 4 U MNase per 200 μl of reaction buffer at 25°C for the indicated period of time.

    Article Title: USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization
    Article Snippet: The nuclear pellet was suspended with 50 μl glycerol buffer (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 5 mM MgAc2 and 25% (vol/vol) glycerol), mixed with equal volume of 2 × MNase buffer (50 mM KCl, 8 mM MgCl2 , 2 mM CaCl2 , and 100 mM Tris-HCl, pH 7.5) and incubated at 37 °C for 5 min with 40 gel Unit of MNase (NEB) per 100 μl of total reaction volume. .. The reaction was stopped by adding EDTA to a final concentration of 10 mM.

    Article Title: The Initial Response of a Eukaryotic Replisome to DNA Damage
    Article Snippet: 20 μL was collected and 1 μL 20-fold diluted MNase (100 U) (New England Biolabs M0247, diluted in 1X MNase buffer, New England Biolabs B0247) added and the mixture incubated at 37°C for 5 min. .. 20 μL was collected and 1 μL 20-fold diluted MNase (100 U) (New England Biolabs M0247, diluted in 1X MNase buffer, New England Biolabs B0247) added and the mixture incubated at 37°C for 5 min.

    Article Title: ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites
    Article Snippet: Digestion of chromatin from untreated, siCTRL- or siAGO2-treated HeLa S3 cells (2 × 106 ) was performed with 50 U of MNase (New England Biolabs) in 300 μl of permeabilization buffer (15 mM Tris–HCl pH 7.4, 300 mM sucrose, 60 mM KCl, 15 mM NaCl, 4 mM CaCl2 , 0.5 mM EGTA, 0.2% NP-40, 0.5 mM β-mercaptoethanol) for 20 min at 37°C. .. Digestion of chromatin from untreated, siCTRL- or siAGO2-treated HeLa S3 cells (2 × 106 ) was performed with 50 U of MNase (New England Biolabs) in 300 μl of permeabilization buffer (15 mM Tris–HCl pH 7.4, 300 mM sucrose, 60 mM KCl, 15 mM NaCl, 4 mM CaCl2 , 0.5 mM EGTA, 0.2% NP-40, 0.5 mM β-mercaptoethanol) for 20 min at 37°C.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C. .. MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM.

    Sequencing:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: As control in sequence analysis, we used DNA fragments obtained from in vitro MNase digestion of purified wild type genomic DNA. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C.

    Article Title: CAL1 is the Drosophila CENP-A assembly factor
    Article Snippet: CENP-A nucleosomes were assembled by Nap1 or CAL11–160 under low salt buffer conditions (10 mM Tris-HCl, pH 7.5, 270 mM NaCl, 2% glycerol, 60 µg/ml BSA, 0.75 mM EDTA, and 0.1 mM DTT) on the 147-bp Widom 601 DNA sequence. .. MNase digestion of nucleosomes was conducted by incubating nucleosomes (∼60 nM) with 2,000 U/ml MNase (New England Biolabs, Inc.) for 30–120 s. After the reactions were stopped by addition of 20 mM EDTA, the samples were treated with 2% SDS and 0.4 mg/ml proteinase K for 30 min at 55°C.

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
    Article Snippet: DNA samples for high throughput sequencing were prepared by the UNC genomics core and 50bp or 100 bp paired ends sequencing was performed using the Illumina platform. .. Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: Paragraph title: Micrococcal nuclease digestion and sequencing (MNase-seq) ... Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C.

    Gel Extraction:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: RNAs and proteins were removed from the sample by intensive treatment first with RNase A and then with proteinase K. Resultant samples were run in 1.2 % agarose gel and the band containing the shortest DNA digestion fragments (around 100 bp) was cut out for subsequent DNA purification with QIAquick Gel Extraction Kit (Qiagen) and sequencing. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C.

    Mouse Assay:

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: Pooled cortices from 10 males and 10 females (total 20 mice) were cross-linked with 1% formaldehyde in PBS for 15 min at room temperature and ChIP was performed using the ChIP-IT High Sensitivity kit (Active Motif) per the manufacturer's instructions, with some modifications: after homogenization using a Dounce homogenizer, nuclei were washed in LB0 buffer (20 mM Tris-HCl [pH7.5], 10 mM NaCl, 1 mM EDTA, 0.2% NP-40, 1 mM PMSF) and resuspended in MNase buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 2.5 mM MgCl2 , 0.1% NP-40, 1 mM DTT, 1 mM PMSF), provided with cOmplete™ EDTA-free protease inhibitor cocktail (Roche Diagnostics). .. After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: For MNase digestion, olfactory neuroepithelia were harvested from Mecp2 WT littermate adult mice and resuspended in PIPES buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, pH 8.0) at 4 °C. .. Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C.

    Chromatin Immunoprecipitation:

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
    Article Snippet: Paragraph title: ChIP-seq and ChIP-PCR ... Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: Chromatin from 5×106 cells per antibody that had been cross-linked with 0.5% formaldehyde for 10 min was isolated by sonication with a Branson sonifier (10 pulses of 10″ at setting 4) in Lysis buffer (50 mM Hepes-KOH, pH 7.5, 1% TritonX-100, 0.1% SDS) and centrifugation for 10′ at 21,000×g . .. To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA. .. Digested chromatin was diluted 3-fold with High Salt ChIP buffer (10 mM Tris-HCl, pH 8, 400 mM NaCl, 1% TritonX-100, 2 mM EDTA, Complete protease inhibitors w/o EDTA (Roche)) to yield 600 μl total volume and incubated overnight at 4°C with either 5 μl of anti-H3 (39163, Active Motif, concentration is not known), 4 μg of anti-H2A.Z (ab4174; Abcam), 1 μg of anti-H3K4me1 (ab8895; Abcam), 1 μg of anti-H3K4me3 (ab8580; Abcam) or 1 μg of H3K27ac (ab4729; Abcam).

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) and quantitative real-time PCR (qPCR) ... After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    Real-time Polymerase Chain Reaction:

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) and quantitative real-time PCR (qPCR) ... After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    Agarose Gel Electrophoresis:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: RNAs and proteins were removed from the sample by intensive treatment first with RNase A and then with proteinase K. Resultant samples were run in 1.2 % agarose gel and the band containing the shortest DNA digestion fragments (around 100 bp) was cut out for subsequent DNA purification with QIAquick Gel Extraction Kit (Qiagen) and sequencing. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C.

    Article Title: Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder
    Article Snippet: The digestion was carried out with MNase (New England BioLabs) at 4 U MNase per 200 μl of reaction buffer at 25°C for the indicated period of time. .. The digestion was carried out with MNase (New England BioLabs) at 4 U MNase per 200 μl of reaction buffer at 25°C for the indicated period of time.

    Article Title: USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization
    Article Snippet: The nuclear pellet was suspended with 50 μl glycerol buffer (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 5 mM MgAc2 and 25% (vol/vol) glycerol), mixed with equal volume of 2 × MNase buffer (50 mM KCl, 8 mM MgCl2 , 2 mM CaCl2 , and 100 mM Tris-HCl, pH 7.5) and incubated at 37 °C for 5 min with 40 gel Unit of MNase (NEB) per 100 μl of total reaction volume. .. The reaction was stopped by adding EDTA to a final concentration of 10 mM.

    Article Title: The Initial Response of a Eukaryotic Replisome to DNA Damage
    Article Snippet: 20 μL was collected and 1 μL 20-fold diluted MNase (100 U) (New England Biolabs M0247, diluted in 1X MNase buffer, New England Biolabs B0247) added and the mixture incubated at 37°C for 5 min. .. 5 volumes of buffer PB (from QIAquick PCR purification kit, QIAGEN) were added and the mixture applied to a QIAquick spin column, washed with buffer PE and eluted in 35 μL water.

    In Vitro:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: As control in sequence analysis, we used DNA fragments obtained from in vitro MNase digestion of purified wild type genomic DNA. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C.

    Homogenization:

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: Pooled cortices from 10 males and 10 females (total 20 mice) were cross-linked with 1% formaldehyde in PBS for 15 min at room temperature and ChIP was performed using the ChIP-IT High Sensitivity kit (Active Motif) per the manufacturer's instructions, with some modifications: after homogenization using a Dounce homogenizer, nuclei were washed in LB0 buffer (20 mM Tris-HCl [pH7.5], 10 mM NaCl, 1 mM EDTA, 0.2% NP-40, 1 mM PMSF) and resuspended in MNase buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 2.5 mM MgCl2 , 0.1% NP-40, 1 mM DTT, 1 mM PMSF), provided with cOmplete™ EDTA-free protease inhibitor cocktail (Roche Diagnostics). .. After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    Next-Generation Sequencing:

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
    Article Snippet: DNA samples for high throughput sequencing were prepared by the UNC genomics core and 50bp or 100 bp paired ends sequencing was performed using the Illumina platform. .. Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C. .. MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX, USA) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6.

    Immunoprecipitation:

    Article Title: HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
    Article Snippet: Paragraph title: HITS-CLIP lysate preparation and immunoprecipitation ... For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract.

    Article Title: Formation of Mobile Chromatin-Associated Nuclear Foci Containing HIV-1 Vpr and VPRBP Is Critical for the Induction of G2 Cell Cycle Arrest
    Article Snippet: Pellets were washed once with nuclease buffer (50 mM Tris pH 8.0, 5 mM CaCl2 , and 100 µg/ml BSA), split in two, and resuspended in nuclease buffer alone or nuclease buffer containing 200 U/ml microccocal nuclease (New England Biolabs, Ipswich, MA, USA). .. Pellets were washed once with nuclease buffer (50 mM Tris pH 8.0, 5 mM CaCl2 , and 100 µg/ml BSA), split in two, and resuspended in nuclease buffer alone or nuclease buffer containing 200 U/ml microccocal nuclease (New England Biolabs, Ipswich, MA, USA).

    Article Title: Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
    Article Snippet: After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C. .. After four pulses of 25 s each, 5 mM CaCl2 and MNase (NEB, 3,000 U in 500 μl reaction mixture) were added and incubated for 10 min at 37°C.

    DNA Purification:

    Article Title: Organization of DNA in a bacterial nucleoid
    Article Snippet: As control in sequence analysis, we used DNA fragments obtained from in vitro MNase digestion of purified wild type genomic DNA. .. The wild type genomic DNA was purified using Wizard Genomic DNA Purification Kit (Promega) and treated with MNase (New England Biolabs) at 12 °C. .. The aliquots were taken out and reaction was stopped at different time points by adding EDTA and incubating with proteinase K for 1 hour at 65 °C.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA, USA) per microlitre volume for 15 min at 37 °C. .. MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM.

    Lysis:

    Article Title: Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum
    Article Snippet: Briefly, schizont‐stage parasites of WT or WT + PfH3p‐HA were isolated from infected erythrocytes by saponin lysis, resuspended in 1 ml of buffer A (10 mM HEPES, pH 7.9, 10 mM KCl, 1.5 mM MgCl2 ) supplemented with protease inhibitors (Complete, Roche), and incubated for 30 min at 4°C. .. Mononucleosomes were prepared from freshly isolated nuclei by digestion with 4 U MNase (NEB) for different amounts of time at 33°C; digestion was stopped by adding 10 mM EGTA pH 8.0.

    Article Title: HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
    Article Snippet: The composition of the SDS lysis buffer was 0.5% SDS, 50mM Tris pH 6.8, 1mM EDTA, 0.125 mg/ml Heparin, 1mM DTT, 1mM PMSF and 1X protease inhibitor (Calbiochem), while RIPA correction buffer was 1.25% NP40, 0.625% sodium deoxycholate, 62.5 mM Tris pH 8.0, 2.25 mM EDTA, 187.5 mM NaCl, 0.125 mg/ml Heparin, 1mM DTT, 1mM PMSF, with 1X protease inhibitors. .. For RNA digestion, MNase (New England Biolabs) was diluted to 10 gel units/μL in RIPA buffer and 5 μL of this freshly diluted 1:200 stock was added to the extract.

    Article Title: Formation of Mobile Chromatin-Associated Nuclear Foci Containing HIV-1 Vpr and VPRBP Is Critical for the Induction of G2 Cell Cycle Arrest
    Article Snippet: Cells were lysed in triton lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.5% Triton X-100, and complete protease inhibitors cocktail (Roche) for 15 minutes. .. Pellets were washed once with nuclease buffer (50 mM Tris pH 8.0, 5 mM CaCl2 , and 100 µg/ml BSA), split in two, and resuspended in nuclease buffer alone or nuclease buffer containing 200 U/ml microccocal nuclease (New England Biolabs, Ipswich, MA, USA).

    Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages
    Article Snippet: Chromatin from 5×106 cells per antibody that had been cross-linked with 0.5% formaldehyde for 10 min was isolated by sonication with a Branson sonifier (10 pulses of 10″ at setting 4) in Lysis buffer (50 mM Hepes-KOH, pH 7.5, 1% TritonX-100, 0.1% SDS) and centrifugation for 10′ at 21,000×g . .. To increase the resolution of ChIP experiments when detecting histones or histone modifications, and to differentiate nucleosome binding from PolII and TBP binding, the isolated chromatin was digested with 0.5 or 1 U MNase (NEB) for 1 h 30′ in the presence of 0.15 mM CaCl2 , and the digestion reaction was stopped by addition of 20 mM EDTA.

    Article Title: m6A-dependent regulation of messenger RNA stability
    Article Snippet: 1 mL lysis buffer (10 mM Tris, pH 7.4, 150 mM KCl, 5 mM MgCl2 , 100 µg/mL CHX, 0.5% Triton-X-100, freshly add 1:100 protease inhibitor, 40 U/mL SUPERasin) was added to suspend the cells and then kept on ice for 15 min with occasional pipetting and rotating. .. 40 µL MNase buffer and 3 µL MNase (6000 gel units, NEB) was added to Portion II .

    Article Title: USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization
    Article Snippet: The lysate was cleared with centrifugation at 2000 × g for 5 min at 4 °C, and then collected and washed with lysis buffer twice. .. The nuclear pellet was suspended with 50 μl glycerol buffer (10 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 5 mM MgAc2 and 25% (vol/vol) glycerol), mixed with equal volume of 2 × MNase buffer (50 mM KCl, 8 mM MgCl2 , 2 mM CaCl2 , and 100 mM Tris-HCl, pH 7.5) and incubated at 37 °C for 5 min with 40 gel Unit of MNase (NEB) per 100 μl of total reaction volume.

    Staining:

    Article Title: CAL1 is the Drosophila CENP-A assembly factor
    Article Snippet: The nucleosomes were analyzed by 6% native PAGE and stained by SYBR gold; the incorporation of H2A–H2B was confirmed by fluorescence imaging of the gel for Alexa Fluor 488. .. MNase digestion of nucleosomes was conducted by incubating nucleosomes (∼60 nM) with 2,000 U/ml MNase (New England Biolabs, Inc.) for 30–120 s. After the reactions were stopped by addition of 20 mM EDTA, the samples were treated with 2% SDS and 0.4 mg/ml proteinase K for 30 min at 55°C.

    Article Title: Histone H3 phosphorylation near the nucleosome dyad alters chromatin structure
    Article Snippet: Reactions were carried out in an initial volume of 10 μl with 10 nM nucleosomes and 0–40 U/ml of MNase (New England Biolabs) in 20 mM Tris, pH 8.0, 0.5 mM CaCl2 at 37°C to prevent H3(T118ph) nucleosome disassembly. .. After 20 min, reactions were quenched with 15 mM EDTA final concentration and resolved by PAGE.

    Clear Native PAGE:

    Article Title: CAL1 is the Drosophila CENP-A assembly factor
    Article Snippet: The nucleosomes were analyzed by 6% native PAGE and stained by SYBR gold; the incorporation of H2A–H2B was confirmed by fluorescence imaging of the gel for Alexa Fluor 488. .. MNase digestion of nucleosomes was conducted by incubating nucleosomes (∼60 nM) with 2,000 U/ml MNase (New England Biolabs, Inc.) for 30–120 s. After the reactions were stopped by addition of 20 mM EDTA, the samples were treated with 2% SDS and 0.4 mg/ml proteinase K for 30 min at 55°C.

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    New England Biolabs mnase
    Mnase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 49 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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